[3dem] Annotation of Protein Modifications in the PDB

[Justin Flatt]

The PDB archive is now including annotation of protein chemical 
modifications (PCMs) and post-translational modifications (PTMs) in a 
standardized way.

As previously announced [1], the PDBx/mmCIF dictionary [2] has been 
extended to enhance PCM and PTM annotation.

This includes new PDBx/mmCIF categories and items as follows:

In the Chemical Component Definition (CCD) files:

  	* A new item in the chem_comp [3] category: chem_comp.pdbx_pcm [4], 
stating whether the CCD is a known PCM/PTM.
  	* A new category called pdbx_chem_comp_pcm [5], stating the PCM/PTM 
type [6] and category [7], as well as on which positions in the amino 
acid and in the polypeptide it is expected to be observed. If this PCM 
is also a known PTM, it will have the Uniprot PTM accession ID.

In the atomic coordinate files:

  	* A new item in the pdbx_entry_details [8] category: 
pdbx_entry_details.has_protein_modification [9], stating if the entry 
contains a PCM/PTM.
  	* A new category called pdbx_modification_feature [10], providing an 
instance-level annotation of all observed PCMs/PTMs within the entry, as 
well as their type and category.

Additionally to providing this new annotation, any protein modifications 
that are inconsistently handled within PDB entries are amended, to 
ensure that a given modification is consistently handled in the PDB 
archive. This includes a major clean-up of incorrect link records 
(struct_conn).

All entries containing protein modifications are being re-released 
gradually from October 2024, throughout Spring 2025.

This standardization ensures that there is a single approach to handling 
each protein modification that occurs within the PDB archive, allowing 
better findability.

Questions or feedback? Contact deposit-help at mail.wwpdb.org.

The protein chemical modifications (PCMs) and post translational 
modifications (PTMs) remediation project is a wwPDB collaborative 
project carried out principally by PDBe [11] at EMBL-EBI [12], and is 
funded by BBSRC grant number BB/V018779/1.

Links:
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[1] https://urldefense.com/v3/__https://www.wwpdb.org/news/news?year=2024*662fa1a565d8a8cacaf76f9c__;Iw!!Mih3wA!Hn5kI7ylJoSTiAouKk2XtwoexbsfQz9uH-Qm94CejIb26fpoW19SVLH8LMGV_DnpPkgW4uoHSWcU55-JGuW0h1_x$ 
[2] https://urldefense.com/v3/__https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/__;!!Mih3wA!Hn5kI7ylJoSTiAouKk2XtwoexbsfQz9uH-Qm94CejIb26fpoW19SVLH8LMGV_DnpPkgW4uoHSWcU55-JGh6Zu0C0$ 
[3] 
https://urldefense.com/v3/__https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/chem_comp.html__;!!Mih3wA!Hn5kI7ylJoSTiAouKk2XtwoexbsfQz9uH-Qm94CejIb26fpoW19SVLH8LMGV_DnpPkgW4uoHSWcU55-JGttIPrUO$ 
[4] 
https://urldefense.com/v3/__https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp.pdbx_pcm.html__;!!Mih3wA!Hn5kI7ylJoSTiAouKk2XtwoexbsfQz9uH-Qm94CejIb26fpoW19SVLH8LMGV_DnpPkgW4uoHSWcU55-JGvrnfA1y$ 
[5] 
https://urldefense.com/v3/__https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_chem_comp_pcm.html__;!!Mih3wA!Hn5kI7ylJoSTiAouKk2XtwoexbsfQz9uH-Qm94CejIb26fpoW19SVLH8LMGV_DnpPkgW4uoHSWcU55-JGlcrj8Pq$ 
[6] 
https://urldefense.com/v3/__https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_pdbx_chem_comp_pcm.type.html__;!!Mih3wA!Hn5kI7ylJoSTiAouKk2XtwoexbsfQz9uH-Qm94CejIb26fpoW19SVLH8LMGV_DnpPkgW4uoHSWcU55-JGs6_-Qmo$ 
[7] 
https://urldefense.com/v3/__https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_pdbx_chem_comp_pcm.category.html__;!!Mih3wA!Hn5kI7ylJoSTiAouKk2XtwoexbsfQz9uH-Qm94CejIb26fpoW19SVLH8LMGV_DnpPkgW4uoHSWcU55-JGnX8skkH$ 
[8] 
https://urldefense.com/v3/__https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_entry_details.html__;!!Mih3wA!Hn5kI7ylJoSTiAouKk2XtwoexbsfQz9uH-Qm94CejIb26fpoW19SVLH8LMGV_DnpPkgW4uoHSWcU55-JGt5TBZKp$ 
[9] 
https://urldefense.com/v3/__https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_pdbx_entry_details.has_protein_modification.html__;!!Mih3wA!Hn5kI7ylJoSTiAouKk2XtwoexbsfQz9uH-Qm94CejIb26fpoW19SVLH8LMGV_DnpPkgW4uoHSWcU55-JGixjrnQh$ 
[10] 
https://urldefense.com/v3/__https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_modification_feature.html__;!!Mih3wA!Hn5kI7ylJoSTiAouKk2XtwoexbsfQz9uH-Qm94CejIb26fpoW19SVLH8LMGV_DnpPkgW4uoHSWcU55-JGkbbaPQp$ 
[11] https://urldefense.com/v3/__https://www.ebi.ac.uk/pdbe/__;!!Mih3wA!Hn5kI7ylJoSTiAouKk2XtwoexbsfQz9uH-Qm94CejIb26fpoW19SVLH8LMGV_DnpPkgW4uoHSWcU55-JGtnysGZ6$ 
[12] https://urldefense.com/v3/__https://www.ebi.ac.uk/__;!!Mih3wA!Hn5kI7ylJoSTiAouKk2XtwoexbsfQz9uH-Qm94CejIb26fpoW19SVLH8LMGV_DnpPkgW4uoHSWcU55-JGoOnKg4G$ 
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